Reference

Bio::Tools::Run::Genscan(3pm)

Object for identifying genes in a given sequence given a matrix(for appropriate organisms).

NAME

Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix(for appropriate organisms).

SYNOPSIS

  # Build a Genscan factory
  my $param = ('MATRIX'=>HumanIso.smat);
  my  $factory = Bio::Tools::Run::Genscan->new($param);
  # Pass the factory a Bio::Seq object
  #@genes is an array of Bio::Tools::Predictions::Gene objects
  my @genes = $factory->run($seq);

DESCRIPTION

Genscan is a gene identifying program developed by Christopher Burge http://genes.mit.edu/burgelab/

By default it looks for an executable called genscan and data/parameter files in the directory specified by the GENSCANDIR environmental variable.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Bala

Email [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

predict_genes()

    Title   :   predict_genes()
    Usage   :   DEPRECATED: use $obj->run($seq) instead 
    Function:   Runs genscan and creates an array of Genes
    Returns :   An array of Bio::Tools::Prediction::Gene objects
    Args    :   A Bio::PrimarySeqI

run

    Title   :   run
    Usage   :   $obj->run($seq)
    Function:   Runs genscan and creates an array of Genes
    Returns :   An array of Bio::Tools::Prediction::Gene objects
    Args    :   A Bio::PrimarySeqI

_run

    Title   :   _run
    Usage   :   $obj->_run()
    Function:   Internal(not to be used directly)
    Returns :   An array of Bio::Tools::Prediction::Gene objects
    Args    :

_set_input()

    Title   :   _set_input
    Usage   :   obj->_set_input($matrixFile,$seqFile)
    Function:   Internal(not to be used directly)
    Returns :  
    Args    :

_writeSeqFile()

    Title   :   _writeSeqFile
    Usage   :   obj->_writeSeqFile($seq)
    Function:   Internal(not to be used directly)
    Returns :   
    Args    :

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